
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LAML-TB/8208756/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/8282706/LAML-TB.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ALL", "-oT=LAML-TB", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=LAML-TB"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/8282706/LAML-TB.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LAML-TB/8208756/transformed.cor.cli.txt"

nPatients in clinical file=200, in cluster file=196, common to both=196
[1]   7 196
[1] "DNMT3A MUTATION ANALYSIS"
[1] 3
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              51              145 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              51              145 
[1] "U2AF1 MUTATION ANALYSIS"
[1] 3
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              8             188 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              8             188 
[1] "FLT3 MUTATION ANALYSIS"
[1] 3
  FLT3 MUTATED FLT3 WILD-TYPE 
            56            140 
  FLT3 MUTATED FLT3 WILD-TYPE 
            56            140 
[1] "IDH2 MUTATION ANALYSIS"
[1] 3
  IDH2 MUTATED IDH2 WILD-TYPE 
            20            176 
  IDH2 MUTATED IDH2 WILD-TYPE 
            20            176 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
            19            177 
  IDH1 MUTATED IDH1 WILD-TYPE 
            19            177 
[1] "NPM1 MUTATION ANALYSIS"
[1] 3
  NPM1 MUTATED NPM1 WILD-TYPE 
            54            142 
  NPM1 MUTATED NPM1 WILD-TYPE 
            54            142 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            15            181 
  NRAS MUTATED NRAS WILD-TYPE 
            15            181 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 6 rows and 196 columns.

Variable 1:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 196 columns, 0 survival variables, and 6 non-survival variables.
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = DNMT3A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DNMT3A MUTATED       38      4      4      1
  DNMT3A WILD-TYPE    105     10     23      2
D1V1, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1             38              105
  CLUS_2              4               10
  CLUS_3              4               23
  CLUS_4              1                2
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DNMT3A MUTATED       25      1     19      1      3
  DNMT3A WILD-TYPE     22     43     46     13     17
D1V2, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  DNMT3A MUTATED       11     20     12
  DNMT3A WILD-TYPE     62     32     33
D1V3, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1             11               62
  CLUS_2             20               32
  CLUS_3             12               33
D1V4, binary
                  cls
clus                0  1
  DNMT3A MUTATED   18 25
  DNMT3A WILD-TYPE 39 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED     18   25
  DNMT3A WILD-TYPE   39   88
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1             18               39
  CLUS_2             25               88
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DNMT3A MUTATED       24      4      5     13
  DNMT3A WILD-TYPE     34     34     37     33
D1V5, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1             24               34
  CLUS_2              4               34
  CLUS_3              5               37
  CLUS_4             13               33
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  DNMT3A MUTATED        2     34     10
  DNMT3A WILD-TYPE     34     46     58
D1V6, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1              2               34
  CLUS_2             34               46
  CLUS_3             10               58

Clustering(2) Variable = U2AF1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  U2AF1 MUTATED        5      0      1      0
  U2AF1 WILD-TYPE    138     14     26      3
D2V1, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             5             138
  CLUS_2             0              14
  CLUS_3             1              26
  CLUS_4             0               3
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  U2AF1 MUTATED        1      0      6      0      1
  U2AF1 WILD-TYPE     46     44     59     14     19
D2V2, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  U2AF1 MUTATED        5      2      0
  U2AF1 WILD-TYPE     68     50     45
D2V3, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             5              68
  CLUS_2             2              50
  CLUS_3             0              45
D2V4, binary
                 cls
clus                0   1
  U2AF1 MUTATED     1   6
  U2AF1 WILD-TYPE  56 107
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF1 MUTATED      1    6
  U2AF1 WILD-TYPE   56  107
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             1              56
  CLUS_2             6             107
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  U2AF1 MUTATED        1      2      4      0
  U2AF1 WILD-TYPE     57     36     38     46
D2V5, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             1              57
  CLUS_2             2              36
  CLUS_3             4              38
  CLUS_4             0              46
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  U2AF1 MUTATED        2      1      4
  U2AF1 WILD-TYPE     34     79     64
D2V6, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             2              34
  CLUS_2             1              79
  CLUS_3             4              64

Clustering(3) Variable = FLT3 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FLT3 MUTATED       51      3      0      0
  FLT3 WILD-TYPE     92     11     27      3
D3V1, multiclass
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  CLUS_1           51             92
  CLUS_2            3             11
  CLUS_3            0             27
  CLUS_4            0              3
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FLT3 MUTATED       26     12      8      2      7
  FLT3 WILD-TYPE     21     32     57     12     13
D3V2, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FLT3 MUTATED        6     20     23
  FLT3 WILD-TYPE     67     32     22
D3V3, multiclass
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  CLUS_1            6             67
  CLUS_2           20             32
  CLUS_3           23             22
D3V4, binary
                cls
clus              0  1
  FLT3 MUTATED   23 26
  FLT3 WILD-TYPE 34 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT3 MUTATED     23   26
  FLT3 WILD-TYPE   34   87
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  CLUS_1           23             34
  CLUS_2           26             87
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FLT3 MUTATED       25      4      7     18
  FLT3 WILD-TYPE     33     34     35     28
D3V5, multiclass
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  CLUS_1           25             33
  CLUS_2            4             34
  CLUS_3            7             35
  CLUS_4           18             28
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FLT3 MUTATED        4     37     13
  FLT3 WILD-TYPE     32     43     55
D3V6, multiclass
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  CLUS_1            4             32
  CLUS_2           37             43
  CLUS_3           13             55

Clustering(4) Variable = IDH2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDH2 MUTATED       14      4      1      0
  IDH2 WILD-TYPE    129     10     26      3
D4V1, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1           14            129
  CLUS_2            4             10
  CLUS_3            1             26
  CLUS_4            0              3
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IDH2 MUTATED        0      0     11      6      1
  IDH2 WILD-TYPE     47     44     54      8     19
D4V2, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH2 MUTATED        8      6      3
  IDH2 WILD-TYPE     65     46     42
D4V3, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            8             65
  CLUS_2            6             46
  CLUS_3            3             42
D4V4, binary
                cls
clus               0   1
  IDH2 MUTATED     6  11
  IDH2 WILD-TYPE  51 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      6   11
  IDH2 WILD-TYPE   51  102
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            6             51
  CLUS_2           11            102
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDH2 MUTATED        5      2      5      5
  IDH2 WILD-TYPE     53     36     37     41
D4V5, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            5             53
  CLUS_2            2             36
  CLUS_3            5             37
  CLUS_4            5             41
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH2 MUTATED        2      7      8
  IDH2 WILD-TYPE     34     73     60
D4V6, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            2             34
  CLUS_2            7             73
  CLUS_3            8             60

Clustering(5) Variable = IDH1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDH1 MUTATED       15      1      1      1
  IDH1 WILD-TYPE    128     13     26      2
D5V1, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           15            128
  CLUS_2            1             13
  CLUS_3            1             26
  CLUS_4            1              2
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IDH1 MUTATED        5      0     10      4      0
  IDH1 WILD-TYPE     42     44     55     10     20
D5V2, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        7      3      6
  IDH1 WILD-TYPE     66     49     39
D5V3, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            7             66
  CLUS_2            3             49
  CLUS_3            6             39
D5V4, binary
                cls
clus               0   1
  IDH1 MUTATED     3  13
  IDH1 WILD-TYPE  54 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      3   13
  IDH1 WILD-TYPE   54  100
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            3             54
  CLUS_2           13            100
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDH1 MUTATED        5      4      2      8
  IDH1 WILD-TYPE     53     34     40     38
D5V5, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            5             53
  CLUS_2            4             34
  CLUS_3            2             40
  CLUS_4            8             38
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        3     11      5
  IDH1 WILD-TYPE     33     69     63
D5V6, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            3             33
  CLUS_2           11             69
  CLUS_3            5             63

Clustering(6) Variable = NPM1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NPM1 MUTATED       52      0      0      0
  NPM1 WILD-TYPE     91     14     27      3
D6V1, multiclass
        clus
vv       NPM1 MUTATED NPM1 WILD-TYPE
  CLUS_1           52             91
  CLUS_2            0             14
  CLUS_3            0             27
  CLUS_4            0              3
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NPM1 MUTATED       36      0      4      9      4
  NPM1 WILD-TYPE     11     44     61      5     16
D6V2, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NPM1 MUTATED        1     22     25
  NPM1 WILD-TYPE     72     30     20
D6V3, multiclass
        clus
vv       NPM1 MUTATED NPM1 WILD-TYPE
  CLUS_1            1             72
  CLUS_2           22             30
  CLUS_3           25             20
D6V4, binary
                cls
clus              0  1
  NPM1 MUTATED   24 24
  NPM1 WILD-TYPE 33 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPM1 MUTATED     24   24
  NPM1 WILD-TYPE   33   89
        clus
vv       NPM1 MUTATED NPM1 WILD-TYPE
  CLUS_1           24             33
  CLUS_2           24             89
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NPM1 MUTATED       37      2      1     12
  NPM1 WILD-TYPE     21     36     41     34
D6V5, multiclass
        clus
vv       NPM1 MUTATED NPM1 WILD-TYPE
  CLUS_1           37             21
  CLUS_2            2             36
  CLUS_3            1             41
  CLUS_4           12             34
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NPM1 MUTATED        0     51      1
  NPM1 WILD-TYPE     36     29     67
D6V6, multiclass
        clus
vv       NPM1 MUTATED NPM1 WILD-TYPE
  CLUS_1            0             36
  CLUS_2           51             29
  CLUS_3            1             67

Clustering(7) Variable = NRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NRAS MUTATED       10      1      3      1
  NRAS WILD-TYPE    133     13     24      2
D7V1, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1           10            133
  CLUS_2            1             13
  CLUS_3            3             24
  CLUS_4            1              2
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NRAS MUTATED        4      3      5      2      1
  NRAS WILD-TYPE     43     41     60     12     19
D7V2, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NRAS MUTATED        5      5      2
  NRAS WILD-TYPE     68     47     43
D7V3, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            5             68
  CLUS_2            5             47
  CLUS_3            2             43
D7V4, binary
                cls
clus               0   1
  NRAS MUTATED     5   7
  NRAS WILD-TYPE  52 106
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      5    7
  NRAS WILD-TYPE   52  106
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            5             52
  CLUS_2            7            106
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NRAS MUTATED        5      3      4      2
  NRAS WILD-TYPE     53     35     38     44
D7V5, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            5             53
  CLUS_2            3             35
  CLUS_3            4             38
  CLUS_4            2             44
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NRAS MUTATED        3      7      4
  NRAS WILD-TYPE     33     73     64
D7V6, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            3             33
  CLUS_2            7             73
  CLUS_3            4             64
> q(save="no")
